Turning his back on legal studies for ordination in the Church of Ireland, Eames embarked on a three-year course at the divinity school in Trinity College, Dublin in 1960, but found the course "intellectually unsatisfying". In 1963 he was appointed curate assistant at Bangor Parish Church, becoming Rector of St Dorothea's in Belfast three years later. In the same year, 1966, he married Christine Daly. During his time in St Dorothea's, in the Braniel and Tullycarnet area of east Belfast, he developed a "coffee bar ministry" among young people but The Troubles interrupted. During this time he rescued a Catholic girl from a loyalist mob who had set her family home on fire. He turned down the opportunity to become dean of Cork and in 1974 was appointed rector of St Mark's in Dundela in east Belfast, formerly C. S. Lewis's family church. On 9 May 1975, at the age of 38, he was elected bishop of the cross-border diocese of Derry and Raphoe – having visited Derry only once. In a groundbreaking move, he invited his similarly young Catholic counterpart, Edward Daly, to his consecration on 9 June. Eames was translated five years later, on 30 May 1980, to the diocese of Down and Dromore. He was elected to Down and Dromore on 23 April and that election confirmed 20 May 1980. In 1986, he became the 103rd Archbishop of Armagh and Primate of All Ireland.

In 1990, some members of the Roman Catholic Church in Ireland felt offended when Eames did not attend the funeral of his neighbour and fellow Armagh primate, Tomás Ó Fiaich. Eames said that the reason for him not attending was due to the necessity of him attending the vote regarding the admission of women to the ordained ministry of the Church of Ireland.[citation needed]

Eames joined the Freemasons as a young man, then later resigned. There is some dispute about when he resigned. The Church of Ireland maintain that he resigned while a curate. In an interview with the Sunday Business Post, the grand secretary of the Freemasons in Ireland said: “Archbishop Eames resigned from his lodges – he was a member of more than one lodge – about the time he was appointed primate."[citation needed]

Drumcree Church, a rural parish near Portadown, became the site of a major political incident in 1996, when the annual Orangemen's march was banned from returning to the centre of Portadown via the Nationalist Garvaghy road after attending worship at Drumcree parish church. This decision was made by the Chief Constable of the Royal Ulster Constabulary and not the Northern Ireland parades commission who did not have authority at this time and were an advisory body only. It was also outwith the remit of the police to forbid worship in the church. The ensuing public unrest and violence escalated and over the next three to four summers the situation in Northern Ireland was very unstable with other parades coming under first police and later commission sanction.

There was great unease in the Church of Ireland as it is truly a broad church in theology and politics and has within its congregations nationalists in the south and unionists in the north and many Orangemen holding office in local parishes. This is not an easy governance and Eames, along with the rector of Dumcree, was damned if he did and damned if he didn't. However it is the perception of many that he did nothing at all. Some bishops in the Republic of Ireland called for Eames to close the parish church. Notable among these was Bishop John Neill who later became Archbishop of Dublin.

Eames refused to do so, believing this action could have precipitated greater unrest and possibly bloodshed. Eames described the Drumcree controversy as his "own personal Calvary". After years of annual unrest in the days leading up to and following "Drumcree Sunday" (the Sunday before 12 July, when Orangemen marched to the church), the dispute continues but the public unrest has decreased by a massive degree, although July and August remain the most dangerous months of the year in Northern Ireland.

Eames is also a significant figure within the general Anglican Communion. In 2003, the self-styled 'divine optimist' was appointed Chairman of the Lambeth Commission on Communion, which examined significant challenges to unity in the Anglican Communion. The Commission published its report ("the Windsor Report") on 18 October 2004.

At the Church of Ireland General Synod in 2006 he announced his intention to retire on 31 December 2006. Church law permitted him to continue as primate until the age of 75 but he resigned, in good health, at the age of 69. On 10 January 2007, the 11 serving bishops of the Church of Ireland, meeting at St Patrick's Cathedral in Dublin, elected Alan Harper, Bishop of Connor, as Eames's successor.

In mid 2007 he was appointed co-chairman, along with Denis Bradley, of the Consultative Group on the Past in Northern Ireland. This aimed to work out how to deal with the legacy of the Troubles in Northern Ireland, especially as it affects the victims of the Troubles and their relatives. This is a very thorny subject, as "One man's freedom fighter is another man's terrorist".

Sources close to the Group created controversy in early 2008 by suggesting that the Troubles could be officially classified as a "war". Relatives of security force victims argued that this would demean the sacrifice of their relatives during the darkest days of the Troubles. Their relatives were often shot when off duty and unable to defend themselves; their opponents were not obeying the rules of war as commonly understood.

Archbishop of Canterbury's Award for Outstanding Service to the Anglican Communion. The Award was presented by the Archbishop of Canterbury, Rowan Williams, on 16 November 2006, at a special service in St Patrick's Cathedral, Armagh. Presenting the award, Archbishop Williams said: “We have in the Anglican Communion various ways of recognising distinguished service. There are awards given at Lambeth, there is the Cross of St Augustine. But once in a while somebody comes along for whom this doesn't seem completely adequate and when Desmond Tutu retired, the then Archbishop of Canterbury invented the Archbishop of Canterbury's Award for Outstanding Service to the Anglican Communion. Tonight it is a huge privilege to present that award for the second time.”

In 2007, he received the Order of Merit from Elizabeth II, this is an exclusive order, restricted to 24 members, who receive it in the personal gift of the Queen, and entitled recipients to the postnominals 'OM' after their name.[2]